- recipe bioconductor-cernanetsim
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/ceRNAnetsim.html
- License:
GPL (>= 3.0)
- Recipe:
This package simulates regulations of ceRNA (Competing Endogenous) expression levels after a expression level change in one or more miRNA/mRNAs. The methodolgy adopted by the package has potential to incorparate any ceRNA (circRNA, lincRNA, etc.) into miRNA:target interaction network. The package basically distributes miRNA expression over available ceRNAs where each ceRNA attracks miRNAs proportional to its amount. But, the package can utilize multiple parameters that modify miRNA effect on its target (seed type, binding energy, binding location, etc.). The functions handle the given dataset as graph object and the processes progress via edge and node variables.
- package bioconductor-cernanetsim¶
- Versions:
1.22.0-0,1.18.0-0,1.14.0-0,1.12.0-0,1.10.0-0,1.6.0-0,1.4.0-0,1.2.1-0,1.2.0-0,1.22.0-0,1.18.0-0,1.14.0-0,1.12.0-0,1.10.0-0,1.6.0-0,1.4.0-0,1.2.1-0,1.2.0-0,1.0.0-0- Depends:
on r-base
>=4.5,<4.6.0a0on r-dplyr
on r-furrr
on r-future
on r-ggplot2
on r-ggraph
on r-igraph
on r-purrr
on r-rlang
on r-tibble
on r-tidygraph
on r-tidyr
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install bioconductor-cernanetsim
to add into an existing workspace instead, run:
pixi add bioconductor-cernanetsim
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install bioconductor-cernanetsim
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-cernanetsim
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/bioconductor-cernanetsim:<tag>
(see bioconductor-cernanetsim/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-cernanetsim/README.html)
